Input and runtime details for job 6038639 (precomputed example)

Sequence input

	sRNA sequences		[.fa]
	Putative target sequences (organism of interest)		[.fa]
	Extract sequences around		start codon
	nt up (1-300)		200
	nt down (1-300)		100

CopraRNA parameters

	Consensus prediction		off
	p-value combination		no
	p-value filtering (0=off)		0

IntaRNA parameters

	Target folding window size		150
	Target max. basepair distance		100

Job ID 6038639 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:35:57 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:19:35 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:35:30 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:35:37 CET 2018
	Job Completed		@ Fri Feb 16 21:35:51 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6038639&toolName=CopraRNA ( 30 days expiry )

Description of the job

IhtA

Output download complete results [zip]

Downloadable files

	CopraRNA result table:		[csv]
	Functional enrichment file		[txt]
	Auxiliary enrichment file		[csv]
	mRNA regions plot		[png] [pdf] [ps]
	sRNA regions plot		[png] [pdf] [ps]
	Functional annotation chart		[html] [pdf]
	Phylogenetic conservation		[png] [pdf]
	16S rDNA tree		[txt] [svg]

mRNA region plot

sRNA region plot

Annot. chart

Conserved, identified interactions for NC_000117 Chlamydia trachomatis D/UW-3/CX

Select: 1-10 11-20 21-30 31-40 41-50 51-60 61-70 71-80 81-90 91-100 101-110 111-120 121-130 131-140 141-150 151-160 161-170 171-180 181-190 191-200 all

Sort by selecting a column name:

Rank	CopraRNA p-value	CopraRNA fdr value	Locus Tag	Gene Name	Energy [kcal/mol]	IntaRNA p-value	Position mRNA	Position sRNA	Annotation
58	0.02303	0.29	ct_184	N/A	-4.35	0.465673	5 -- 18	18 -- 35	Holliday junction resolvase	_____________4__________________19\n_____________\|__________________\|\n_______5'-ACGU_______AA_________AUUAA...UGC-3'\n______________UUAGAAG______CAUGG\n______________\|:\|\|\|\|\|______\|\|\|\|\|\n______________AGUCUUC______GUACC\n3'-UUU...AUCUC_______GAUAAG_____GCAAU...GAA-5'\n_____________\|__________________\|\n_____________36_________________17\n	5 -- 11	29 -- 35	-12.193 kcal/mol	2.86148 kcal/mol	4.97803 kcal/mol	4 19@LB@ \| \|@LB@ 5'-ACGU AA AUUAA...UGC-3'@LB@ UUAGAAG CAUGG@LB@ \|:\|\|\|\|\| \|\|\|\|\|@LB@ AGUCUUC GUACC@LB@3'-UUU...AUCUC GAUAAG GCAAU...GAA-5'@LB@ \| \|@LB@ 36 17@LB@@LB@@LB@Energy -4.35 kcal/mol@LB@Hybridization Energy -12.193 kcal/mol@LB@Unfolding Energy - mRNA 2.86148 kcal/mol@LB@Unfolding Energy - sRNA 4.97803 kcal/mol@LB@@LB@Position - mRNA 5 -- 18@LB@Position - sRNA 18 -- 35@LB@Position Seed - mRNA 5 -- 11@LB@Position Seed - sRNA 29 -- 35@LB@
90	0.03275	0.2942	ct_332	pykF	-4.34	0.468844	109 -- 116	80 -- 87	pyruvate kinase	_____________108______117\n_____________\|________\|\n5'-UUU...GCGAU________CUAAA...GCC-3'\n______________UGCGGUUG\n______________\|:\|\|\|:\|:\n______________AUGCCGAU\n3'-UUU...CCUCU________UGAGG...GAA-5'\n_____________\|________\|\n_____________88_______79\n	110 -- 116	80 -- 86	-9.21836 kcal/mol	3.78563 kcal/mol	1.09752 kcal/mol	108 117@LB@ \| \|@LB@5'-UUU...GCGAU CUAAA...GCC-3'@LB@ UGCGGUUG@LB@ \|:\|\|\|:\|:@LB@ AUGCCGAU@LB@3'-UUU...CCUCU UGAGG...GAA-5'@LB@ \| \|@LB@ 88 79@LB@@LB@@LB@Energy -4.34 kcal/mol@LB@Hybridization Energy -9.21836 kcal/mol@LB@Unfolding Energy - mRNA 3.78563 kcal/mol@LB@Unfolding Energy - sRNA 1.09752 kcal/mol@LB@@LB@Position - mRNA 109 -- 116@LB@Position - sRNA 80 -- 87@LB@Position Seed - mRNA 110 -- 116@LB@Position Seed - sRNA 80 -- 86@LB@
100	0.03658	0.3007	ct_875	N/A	-4.31	0.472369	272 -- 278	28 -- 34		_____________271_____279\n_____________\|_______\|\n5'-GGG...AAUCG_______CAAAA...AUA-3'\n______________CAGAAGU\n______________\|\|\|\|\|\|:\n______________GUCUUCG\n3'-UUU...UCUCA_______AUAAG...GAA-5'\n_____________\|_______\|\n_____________35______27\n	272 -- 278	28 -- 34	-8.98313 kcal/mol	0.5541 kcal/mol	4.11458 kcal/mol	271 279@LB@ \| \|@LB@5'-GGG...AAUCG CAAAA...AUA-3'@LB@ CAGAAGU@LB@ \|\|\|\|\|\|:@LB@ GUCUUCG@LB@3'-UUU...UCUCA AUAAG...GAA-5'@LB@ \| \|@LB@ 35 27@LB@@LB@@LB@Energy -4.31 kcal/mol@LB@Hybridization Energy -8.98313 kcal/mol@LB@Unfolding Energy - mRNA 0.5541 kcal/mol@LB@Unfolding Energy - sRNA 4.11458 kcal/mol@LB@@LB@Position - mRNA 272 -- 278@LB@Position - sRNA 28 -- 34@LB@Position Seed - mRNA 272 -- 278@LB@Position Seed - sRNA 28 -- 34@LB@
196	0.08741	0.3657	ct_698	N/A	-4.23	0.486304	280 -- 292	22 -- 34	tRNA modification GTPase	_____________279___________293\n_____________\|_____________\|\n5'-AAA...CGGAC____U________UAUUUCUG-3'\n______________CGGA_GCUAUUUC\n______________\|:\|\|_\|\|\|\|\|\|:\|\n______________GUCU_CGAUAAGG\n3'-UUU...UCUCA____U________UACCG...GAA-5'\n_____________\|_____________\|\n_____________35____________21\n	285 -- 291	23 -- 29	-13.8571 kcal/mol	4.89721 kcal/mol	4.72608 kcal/mol	279 293@LB@ \| \|@LB@5'-AAA...CGGAC U UAUUUCUG-3'@LB@ CGGA GCUAUUUC@LB@ \|:\|\| \|\|\|\|\|\|:\|@LB@ GUCU CGAUAAGG@LB@3'-UUU...UCUCA U UACCG...GAA-5'@LB@ \| \|@LB@ 35 21@LB@@LB@@LB@Energy -4.23 kcal/mol@LB@Hybridization Energy -13.8571 kcal/mol@LB@Unfolding Energy - mRNA 4.89721 kcal/mol@LB@Unfolding Energy - sRNA 4.72608 kcal/mol@LB@@LB@Position - mRNA 280 -- 292@LB@Position - sRNA 22 -- 34@LB@Position Seed - mRNA 285 -- 291@LB@Position Seed - sRNA 23 -- 29@LB@
99	0.03647	0.3007	ct_810	rl32	-4.11	0.507281	35 -- 46	46 -- 58	50S ribosomal protein L32	_____________34____________47\n_____________\|_____________\|\n5'-UUC...CAAGU_____________CGUUU...GCA-3'\n______________CUUCCUG_GUAUA\n______________\|::\|\|\|\|_\|\|\|:\|\n______________GGGGGAC_CAUGU\n3'-UUU...UGAAG_______A_____UUGUG...GAA-5'\n_____________\|_____________\|\n_____________59____________45\n	35 -- 41	52 -- 58	-13.0221 kcal/mol	1.6119 kcal/mol	7.29598 kcal/mol	34 47@LB@ \| \|@LB@5'-UUC...CAAGU CGUUU...GCA-3'@LB@ CUUCCUG GUAUA@LB@ \|::\|\|\|\| \|\|\|:\|@LB@ GGGGGAC CAUGU@LB@3'-UUU...UGAAG A UUGUG...GAA-5'@LB@ \| \|@LB@ 59 45@LB@@LB@@LB@Energy -4.11 kcal/mol@LB@Hybridization Energy -13.0221 kcal/mol@LB@Unfolding Energy - mRNA 1.6119 kcal/mol@LB@Unfolding Energy - sRNA 7.29598 kcal/mol@LB@@LB@Position - mRNA 35 -- 46@LB@Position - sRNA 46 -- 58@LB@Position Seed - mRNA 35 -- 41@LB@Position Seed - sRNA 52 -- 58@LB@
144	0.05714	0.3262	ct_392	yprS	-4.10	0.509599	238 -- 247	22 -- 33		_____________237__________248\n_____________\|____________\|\n5'-AGG...CCCUG____________CAAUU...GUC-3'\n______________AGAGGCU__UCC\n______________\|\|\|:\|\|\|__\|\|\|\n______________UCUUCGA__AGG\n3'-UUU...CUCAG_______UA___UACCG...GAA-5'\n_____________\|____________\|\n_____________34___________21\n	238 -- 244	27 -- 33	-11.7781 kcal/mol	2.9519 kcal/mol	4.72509 kcal/mol	237 248@LB@ \| \|@LB@5'-AGG...CCCUG CAAUU...GUC-3'@LB@ AGAGGCU UCC@LB@ \|\|\|:\|\|\| \|\|\|@LB@ UCUUCGA AGG@LB@3'-UUU...CUCAG UA UACCG...GAA-5'@LB@ \| \|@LB@ 34 21@LB@@LB@@LB@Energy -4.10 kcal/mol@LB@Hybridization Energy -11.7781 kcal/mol@LB@Unfolding Energy - mRNA 2.9519 kcal/mol@LB@Unfolding Energy - sRNA 4.72509 kcal/mol@LB@@LB@Position - mRNA 238 -- 247@LB@Position - sRNA 22 -- 33@LB@Position Seed - mRNA 238 -- 244@LB@Position Seed - sRNA 27 -- 33@LB@
169	0.07086	0.3447	ct_615	sigA	-4.07	0.514760	248 -- 272	10 -- 33	RNA polymerase sigma factor	_____________247________________________273\n_____________\|__________________________\|\n5'-GGU...CAAGA_____AAA_____AAGAAA_______GAGUU...AAG-3'\n______________AGAAG____UCCA______GUUAGAA\n______________\|\|\|\|\|____\|\|\|\|______\|\|\|\|\|\|\|\n______________UCUUC____AGGU______CAAUCUU\n3'-UUU...CUCAG_____GAUA____ACCG_________AUGGU...GAA-5'\n_____________\|__________________________\|\n_____________34_________________________9\n	266 -- 272	10 -- 16	-15.5151 kcal/mol	2.85327 kcal/mol	8.5898 kcal/mol	247 273@LB@ \| \|@LB@5'-GGU...CAAGA AAA AAGAAA GAGUU...AAG-3'@LB@ AGAAG UCCA GUUAGAA@LB@ \|\|\|\|\| \|\|\|\| \|\|\|\|\|\|\|@LB@ UCUUC AGGU CAAUCUU@LB@3'-UUU...CUCAG GAUA ACCG AUGGU...GAA-5'@LB@ \| \|@LB@ 34 9@LB@@LB@@LB@Energy -4.07 kcal/mol@LB@Hybridization Energy -15.5151 kcal/mol@LB@Unfolding Energy - mRNA 2.85327 kcal/mol@LB@Unfolding Energy - sRNA 8.5898 kcal/mol@LB@@LB@Position - mRNA 248 -- 272@LB@Position - sRNA 10 -- 33@LB@Position Seed - mRNA 266 -- 272@LB@Position Seed - sRNA 10 -- 16@LB@
111	0.04436	0.3262	ct_405	ribC	-3.97	0.532190	3 -- 10	49 -- 56	riboflavin synthase	_____________2________11\n_____________\|________\|\n_________5'-AA________CUUGU...AUG-3'\n______________UCCUGUGU\n______________:\|\|\|\|\|\|\|\n______________GGGACACA\n3'-UUU...AAGGG________UGUUU...GAA-5'\n_____________\|________\|\n_____________57_______48\n	4 -- 10	49 -- 55	-11.4476 kcal/mol	0.227857 kcal/mol	7.24525 kcal/mol	2 11@LB@ \| \|@LB@ 5'-AA CUUGU...AUG-3'@LB@ UCCUGUGU@LB@ :\|\|\|\|\|\|\|@LB@ GGGACACA@LB@3'-UUU...AAGGG UGUUU...GAA-5'@LB@ \| \|@LB@ 57 48@LB@@LB@@LB@Energy -3.97 kcal/mol@LB@Hybridization Energy -11.4476 kcal/mol@LB@Unfolding Energy - mRNA 0.227857 kcal/mol@LB@Unfolding Energy - sRNA 7.24525 kcal/mol@LB@@LB@Position - mRNA 3 -- 10@LB@Position - sRNA 49 -- 56@LB@Position Seed - mRNA 4 -- 10@LB@Position Seed - sRNA 49 -- 55@LB@
178	0.07667	0.3541	ct_386	N/A	-3.82	0.559485	134 -- 140	82 -- 88		_____________133_____141\n_____________\|_______\|\n5'-CUU...UUUGG_______ACUAC...AGA-3'\n______________AUAUGGU\n______________\|\|\|:\|\|:\n______________UAUGCCG\n3'-UUU...GCCUC_______AUUGA...GAA-5'\n_____________\|_______\|\n_____________89______81\n	134 -- 140	82 -- 88	-6.88346 kcal/mol	1.9622 kcal/mol	1.09753 kcal/mol	133 141@LB@ \| \|@LB@5'-CUU...UUUGG ACUAC...AGA-3'@LB@ AUAUGGU@LB@ \|\|\|:\|\|:@LB@ UAUGCCG@LB@3'-UUU...GCCUC AUUGA...GAA-5'@LB@ \| \|@LB@ 89 81@LB@@LB@@LB@Energy -3.82 kcal/mol@LB@Hybridization Energy -6.88346 kcal/mol@LB@Unfolding Energy - mRNA 1.9622 kcal/mol@LB@Unfolding Energy - sRNA 1.09753 kcal/mol@LB@@LB@Position - mRNA 134 -- 140@LB@Position - sRNA 82 -- 88@LB@Position Seed - mRNA 134 -- 140@LB@Position Seed - sRNA 82 -- 88@LB@
79	0.0288	0.29	ct_431	clpP_1	-3.71	0.580570	128 -- 134	79 -- 85	ATP-dependent Clp protease proteolytic subunit	_____________127_____135\n_____________\|_______\|\n5'-GAA...ACGUG_______UUUAU...AAA-3'\n______________UGGCUGA\n______________:\|\|\|\|:\|\n______________GCCGAUU\n3'-UUU...UCUAU_______GAGGU...GAA-5'\n_____________\|_______\|\n_____________86______78\n	128 -- 134	79 -- 85	-7.88567 kcal/mol	3.08 kcal/mol	1.09751 kcal/mol	127 135@LB@ \| \|@LB@5'-GAA...ACGUG UUUAU...AAA-3'@LB@ UGGCUGA@LB@ :\|\|\|\|:\|@LB@ GCCGAUU@LB@3'-UUU...UCUAU GAGGU...GAA-5'@LB@ \| \|@LB@ 86 78@LB@@LB@@LB@Energy -3.71 kcal/mol@LB@Hybridization Energy -7.88567 kcal/mol@LB@Unfolding Energy - mRNA 3.08 kcal/mol@LB@Unfolding Energy - sRNA 1.09751 kcal/mol@LB@@LB@Position - mRNA 128 -- 134@LB@Position - sRNA 79 -- 85@LB@Position Seed - mRNA 128 -- 134@LB@Position Seed - sRNA 79 -- 85@LB@

Details of Selected Interaction Download Interaction Details

mRNA

sRNA

Energy

Hybridization Energy

Unfolding Energy - mRNA

Unfolding Energy - sRNA

Position - mRNA

Position - sRNA

Position Seed - mRNA

Position Seed - sRNA

Evolutionary conservation of mRNA targets (alignment generated with Jalview)

Evolutionary conservation of sRNA (alignment generated with Jalview)

Job resubmission

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service.

When using CopraRNA please cite :

Patrick R. Wright, Jens Georg, Martin Mann, Dragos A. Sorescu, Andreas S. Richter, Steffen Lott, Robert Kleinkauf, Wolfgang R. Hess, and Rolf Backofen
CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains
Nucleic Acids Research, 2014, 42 (W1), W119-W123.
Patrick R. Wright, Andreas S. Richter, Kai Papenfort, Martin Mann, Joerg Vogel, Wolfgang R. Hess, Rolf Backofen and Jens Georg
Comparative genomics boosts target prediction for bacterial small RNAs
Proc Natl Acad Sci USA, 2013, 110 (37), E3487-E3496.
Martin Raden, Syed M Ali, Omer S Alkhnbashi, Anke Busch, Fabrizio Costa, Jason A Davis, Florian Eggenhofer, Rick Gelhausen, Jens Georg, Steffen Heyne, Michael Hiller, Kousik Kundu, Robert Kleinkauf, Steffen C Lott, Mostafa M Mohamed, Alexander Mattheis, Milad Miladi, Andreas S Richter, Sebastian Will, Joachim Wolff, Patrick R Wright, and Rolf Backofen
Freiburg RNA tools: a central online resource for RNA-focused research and teaching
Nucleic Acids Research, 46(W1), W25-W29, 2018.

Results are computed with CopraRNA version 2.1.2

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